mtDNA

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PhyloTree.org

January 14, 2010 in Anthropology, Genetics by Kris | 1 comment

ResearchBlogging.orgAs a grad student in anthropological genetics, one of the more tedious tasks I had was aligning mtDNA sequences manually, noting the mutations (differences from the revised Cambridge Reference Sequence, which belongs to haplogroup H), and determining the haplogroup (or lineage).  The difficulty was compounded by a lack of comprehensive definitions.  I had a stack of references listing diagnostic mutations, but not for every haplogroup, not even for the subset of haplogroups found in Europe, which was the focus of my research. Part of the problem was that when I started whole genome sequencing wasn’t available. Whenever a new haplogroup was discovered, the authors would name it, and in some cases the same name was given to different sequences because there was no standardized nomenclature. What I needed was a phylogenetic tree, showing the relationships between lineages, and all diagnostic mutations for each haplogroup.

That’s what you can find at PhyloTree.org.  The “updated comprehensive phylogenetic tree of global human mitochondrial DNA variation” lists all mitochondrial haplogroups, with diagnostic mutations from both the coding and control regions, based on full sequences deposited in GenBank. The figure below shows a portion of the tree for Haplogroup H1a:

Haplogroup H1a. Coding region mutations are in black, control region mutations in blue.

Coding region mutations are in black, control region mutations in blue.  Established haplogroup names are in in black at the base of the branches, and proposed haplogroup labels are shown in red.  GenBank accession numbers are provided at the tips of the branches. Assigning haplogroups to your samples is as easy as using the find function in your Internet brower. PhyloTree is continuously updated as new sequences are published; they’re currently on Build 7.0 as of November 2009.

PhyloTree is a valuable and much need resource for the anthropological genetics community, especially poor grad students.
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van Oven, M., & Kayser, M. (2009). Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation Human Mutation, 30 (2) DOI: 10.1002/humu.20921

Counting Your Chickens….

August 28, 2008 in Anthropology, Genetics by Kris | 1 comment

ResearchBlogging.orgLast summer, I wrote this post on the possible Polynesian origin of South American chickens. In July, Gongora et al published a response to that study, titled “Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA.”

The authors sequenced the HVS-I region of 41 modern Chilean chickens, and compared their data to ~1000 published modern and ancient sequences.  Contrary to Storey et als data, the prehistoric sequences were found to belong to the “single most common chicken haplotype found” worldwide, a haplotype which also includes common Asian and European varieties.

The authors of the present study also note that if the prehistoric dates are calibrated to account for proximity to a marine environment, which in archaeological terms:

can exhibit older apparent radiocarbon ages because of the uptake of carbon that has already undergone radioactive decay though long residence times in the deep ocean (10309)

then the dates for the Chilean chicken samples from El Arenal could be securely dated as Pre-Columbian only if less than 20% of the diet came from marine sources.

Looks like Storey’s team has a ways to go to prove a Polynesian origin for New World chickens.

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Gongora J, Rawlence NJ, Mobegi VA, Jianlin H, Alcalde JA, Matus JT, Hanotte O, Moran C, Austin JJ, Ulm S, Anderson AJ, Larson G, & Cooper A (2008). Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proceedings of the National Academy of Sciences of the United States of America, 105 (30), 10308-13 PMID: 18663216

How did the Chicken Cross the Ocean?

June 8, 2007 in Anthropology, Evolution, Genetics, Technology, Uncategorized by Kris | 1 comment

ResearchBlogging.org An old joke, but serious business for anthropologists and archaeologists studying the introduction of poultry to South America. Introduction of chickens to South America by European explorers had been proposed (or assumed), but Pizarro documented the presence of chickens among the Inca at contact. Researchers at the University of Aukland, using commensal modeling (studying distribution patterns of animals typically found with humans, such as rats, dogs, and domestic species), came to an interesting conclusion published this week in the Proceedings of the National Academy of Sciences.

Examining mitochondrial DNA sequences from 12 samples collected at El-Arenal-1 in Chile, Alice Storey and colleagues found that the sequences match those found at prehistoric sites in Polynesia – Mele Havea in Tonga (2,000-1,550 BP) and Fatu-ma-Futi in American Samoa (AD 700-1390). The chicken bones found at El Arenal-1 were radiocarbon dated to between 1304-1424 AD, meaning they were present on the west coast of South America prior to Spanish or Portuguese contact on the east coast of the continent around AD 1500.

Map of Polynesia

Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile is an important study in two ways. One, it provides the first direct proof of Polynesian contact with South America. (See this post). And since chickens aren’t known for being great fliers, they must have instead come by boat, or in this case, Polynesian sewn plank canoes. Two, it demonstrates what DNA analysis of other types of archaeological remains (not just human) can tell us about human migration patterns.

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Image adapted from Storey, A., Ramirez, J., Quiroz, D., Burley, D., Addison, D., Walter, R., Anderson, A., Hunt, T., Athens, J., Huynen, L., & Matisoo-Smith, E. (2007). Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile Proceedings of the National Academy of Sciences, 104 (25), 10335-10339 DOI: 10.1073/pnas.0703993104

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